The Presbyterian Church of Korea was established in 1907. In 1912, the first general assembly was held. Presbyterian missionaries from Australia, the United States and Canada came to Korea in increasing numbers in the following years. During the Japanese occupation (1910-1945) the church faced many difficulties. As Japan increased its pressure on Koreans by banning the use of the Korean language and Korean names, it also attempted to force Christians to worship at the Shinto shrine. In 1953 the Presbyterian Church faced another serious challenge, centred around theology and methods of biblical study taught at the then Chosun Theological Seminary, now the Graduate School of Theology, Hanshin University. It developed into a conflict between two groups, those who were influenced by the conservative, fundamentalist theology propounded by the missionaries, including the leadership of the church, and those who stood for the freedom of learning theology and methods of historical critical interpretation of the Bible. The seminary upheld the theological tradition of Calvin and the Reformation and the faculty were deeply committed to developing higher theological education and articulating Christian theology from a Korean perspective. The conservative and fundamentalist faction would not accept this theology and the difference between the two groups became irreconcilable. The conflict divided the Presbyterians in 1953 into the Presbyterian Church in the Republic of Korea (PROK) and the Presbyterian Church of Korea (PCK).

The PROK is committed to participating in Missio Dei, God's salvation work in society and history. It upholds the spiritual importance of dialogue, engagement, diversity, and reconciliation. It has been serving the poor and the marginalized, the "Minjung", such as the disabled, farmers, the elderly, orphans, undocumented migrant workers, homeless teenagers, sex workers and, particularly since the implosion of the national economy, the unemployed and their families. The PROK has been a prophetic voice for democratization, human rights and reunification, protesting courageously against military dictatorship government. It took the initiative in sending humanitarian food aid, as well as funds, equipment and machinery to North Korea.

The PROK has developed an enduring commitment to ecumenism with strong partnerships with many churches around the world. It was the first Presbyterian denomination to ordain women as elders in 1956 and as ministers in 1974. It elected a woman elder as the lay vice-moderator of the 83rd general assembly in 1998, a first in Korean Presbyterian history. Recognizing that sectarianism is a serious problem facing the whole Presbyterian church, the PROK has led the dialogue among Presbyterian denominations which has resulted in the formation of the Council of Presbyterian Churches.

In 2003 with a major celebration of the milestone jubilee year, the PROK launched a Jubilee proclamation which declares its mission task to be:

To work for justice and peace by restoring earth's destroyed nature to the order of God's creation, so that the earth may become a true community of life.

To transform a culture of materialism and violence into a culture of life.

To work for reconciliation and peaceful reunification of our divided people.

To make every effort to unite the churches separated by division into "One Church".

To renew the church, that it may become the whole and perfect body of Christ.

To build equality between men and women and harmony between generations.